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comparison SMART/galaxy/getWigProfile.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="getWigProfile" name="get WIG profile"> 1 <tool id="getWigProfile" name="get wig profile">
2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description> 2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/getWigProfile.py -i $formatType.inputFileName 4 ../Java/Python/getWigProfile.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
65 </conditional> 62 </conditional>
66 63
67 </inputs> 64 </inputs>
68 65
69 <outputs> 66 <outputs>
70 <data name="outputFilePNG" format="png" label="[get WIG profile] output file"/> 67 <data name="outputFilePNG" format="png" label="[getWigProfile]out file"/>
71 </outputs> 68 </outputs>
72 69
73 <help>
74 Computes the average distribution of the WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) along the transcripts given in input, and possibly before and after the transcripts.
75
76 The main inputs of the functions are a file containing a list of transcripts (or any sets of genomic interval) and a directory containing a set of WIG files (one file per chromosome, or one file per chromosome and per strand). The function then computes the WIG profile of each transcript. The user can also define a region around the transcripts that should also be plotted (in this case, the profile will include the WIG values which overlap with the transcript as well as the 5' and 3' regions). Since the transcript do not necessarily have the same sizes, all profiles will be extended or shrinked to fit in a size which is given by the user. If the resulting profile is a bit bumpy, the user can also smoothen the curve by using a linear smoothing function (the size of the smoothing window is given by the user). Finally, the user may want to plot the WIG data for the opposite strand too (if the strand specific WUG data are available).
77 </help>
78 </tool> 70 </tool>